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The 36-year-old actor plays nefarious slave owner Edwin Epps in the historical drama and admits he had to keep practising with the weapon to perfect his skills so the punishment of his slaves was realistic on screen.
Fassbender found it uncomfortable to play a man so readily willing to inflict pain on other humans in order to control them but he believes his dedication to mastering the tool is apparent to everyone who sees the acclaimed movie.
He told Britain's GQ magazine: "I remember I had to practise on the whip; I had to learn to crack it properly. I remember thinking about the knot it created in my shoulder, the knot it would create from doing such a physical task as whipping the skin off another human's back.
"That physical memory would stay in the body, my body, Epps' body. The body would retain the memory of what you have done to your fellow man or fellow woman. What would the psychological effect of this be? The retention of pain in your body memory? It's got to be stored somewhere. That's what I tried to with Epps. There's a deep conflict in the man."
Steve McQueen's film is based on the 1853 autobiography by Solomon Northup, a Negro man who was born free in New York State but was kidnapped in Washington, D.C. in 1841 and sold into slavery.
The movie also stars Chiwetel Ejiofor, who plays Northup, Benedict Cumberbatch, Paul Giamatti, Brad Pitt and Sarah Paulson.
